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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-07-10, 20:33 CEST based on data in: /gpfs1/work/zarski/arabid_tiwari/skripts/work/a2/83d2109e970ae20970cb7130759e1e


        General Statistics

        Showing 0/72 rows and 22/35 columns.
        Sample NamedupInt% rRNADuplication5'-3' biasM AlignedProper PairsError rateNon-primaryReads mapped% Mapped% Proper pairs% MapQ 0 readsTotal seqsReadsReads mapped% Reads mappedTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedDupsGCAvg lenMedian lenFailedSeqsTrimmed basesDupsGCAvg lenMedian lenFailedSeqs
        SRX7222823
        0.1
        2.8
        73.6%
        2.01
        4.1M
        0.0%
        0.41%
        6.9M
        4.1M
        100.0%
        0.0%
        14.7%
        4.1M
        11.1M
        11.1M
        100.0%
        4.4M
        4.1M
        94.1%
        1.7M
        39.9%
        2.4M
        68.5%
        45.0%
        22bp
        21bp
        40%
        6.4M
        1.8%
        64.4%
        44.0%
        23bp
        22bp
        30%
        4.4M
        SRX7222824
        0.1
        3.7
        71.5%
        2.05
        6.5M
        0.0%
        0.90%
        11.0M
        6.5M
        100.0%
        0.0%
        14.3%
        6.5M
        17.5M
        17.5M
        100.0%
        7.2M
        6.5M
        91.1%
        2.8M
        38.4%
        3.8M
        55.1%
        46.0%
        22bp
        22bp
        20%
        7.5M
        2.5%
        57.1%
        46.0%
        22bp
        22bp
        30%
        7.2M
        SRX7222825
        0.1
        6.4
        74.5%
        2.16
        8.6M
        0.0%
        1.00%
        14.5M
        8.6M
        100.0%
        0.0%
        12.7%
        8.6M
        23.1M
        23.1M
        100.0%
        9.5M
        8.6M
        90.8%
        3.1M
        32.3%
        5.5M
        60.0%
        46.0%
        22bp
        22bp
        20%
        9.9M
        2.4%
        61.9%
        46.0%
        22bp
        22bp
        30%
        9.5M
        SRX7222826
        0.0
        4.2
        77.7%
        1.74
        6.6M
        0.0%
        0.57%
        12.2M
        6.6M
        100.0%
        0.0%
        13.6%
        6.6M
        18.8M
        18.8M
        100.0%
        7.2M
        6.6M
        91.0%
        2.3M
        32.4%
        4.2M
        58.9%
        46.0%
        25bp
        24bp
        20%
        8.0M
        1.6%
        60.8%
        46.0%
        25bp
        24bp
        30%
        7.2M
        SRX7222827
        0.1
        4.4
        74.8%
        1.59
        7.9M
        0.0%
        0.75%
        15.1M
        7.9M
        100.0%
        0.0%
        15.9%
        7.9M
        23.0M
        23.0M
        100.0%
        9.0M
        7.9M
        88.2%
        3.3M
        37.4%
        4.6M
        56.5%
        45.0%
        24bp
        24bp
        30%
        9.1M
        2.2%
        58.5%
        46.0%
        24bp
        23bp
        30%
        9.0M
        SRX7222828
        0.1
        4.6
        76.0%
        2.68
        6.9M
        0.0%
        0.94%
        12.1M
        6.9M
        100.0%
        0.0%
        13.4%
        6.9M
        18.9M
        18.9M
        100.0%
        7.8M
        6.9M
        88.7%
        2.6M
        33.5%
        4.3M
        58.9%
        45.0%
        23bp
        23bp
        20%
        8.1M
        2.4%
        60.8%
        46.0%
        23bp
        22bp
        30%
        7.8M
        SRX7222829
        0.0
        2.5
        76.6%
        1.54
        6.6M
        0.0%
        0.49%
        12.5M
        6.6M
        100.0%
        0.0%
        13.5%
        6.6M
        19.1M
        19.1M
        100.0%
        7.3M
        6.6M
        90.2%
        2.4M
        33.3%
        4.2M
        53.6%
        46.0%
        25bp
        24bp
        10%
        8.8M
        1.7%
        53.3%
        46.0%
        26bp
        24bp
        30%
        7.3M
        SRX7222830
        0.1
        4.4
        70.5%
        1.72
        7.3M
        0.0%
        0.83%
        13.6M
        7.3M
        100.0%
        0.0%
        17.5%
        7.3M
        20.9M
        20.9M
        100.0%
        8.0M
        7.3M
        90.8%
        3.1M
        38.0%
        4.3M
        51.1%
        44.0%
        23bp
        22bp
        20%
        8.4M
        2.5%
        53.2%
        44.0%
        22bp
        22bp
        30%
        8.0M
        SRX7222831
        0.1
        7.5
        74.9%
        1.94
        8.7M
        0.0%
        1.07%
        14.2M
        8.7M
        100.0%
        0.0%
        11.4%
        8.7M
        22.9M
        22.9M
        100.0%
        10.1M
        8.7M
        85.4%
        3.1M
        30.5%
        5.6M
        55.3%
        46.0%
        24bp
        24bp
        20%
        10.4M
        2.3%
        57.6%
        46.0%
        24bp
        23bp
        30%
        10.1M
        SRX7222832
        0.1
        8.6
        68.5%
        2.23
        2.0M
        0.0%
        1.13%
        3.0M
        2.0M
        100.0%
        0.0%
        9.8%
        2.0M
        5.0M
        5.0M
        100.0%
        2.4M
        2.0M
        84.3%
        0.7M
        29.8%
        1.3M
        48.0%
        46.0%
        24bp
        24bp
        10%
        2.5M
        2.3%
        50.4%
        47.0%
        24bp
        23bp
        30%
        2.4M
        SRX7222833
        0.1
        0.1
        57.2%
        1.08
        11.3M
        38.5%
        0.23%
        1.1M
        22.6M
        100.0%
        100.0%
        0.0%
        22.6M
        23.8M
        23.8M
        100.0%
        11.4M
        11.3M
        99.4%
        10.8M
        94.7%
        0.5M
        SRX7222833_1
        78.1%
        42.0%
        150bp
        150bp
        10%
        11.4M
        0.6%
        78.1%
        42.0%
        149bp
        150bp
        20%
        11.4M
        SRX7222833_2
        75.3%
        42.0%
        150bp
        150bp
        40%
        11.4M
        0.9%
        75.3%
        42.0%
        149bp
        150bp
        40%
        11.4M
        SRX7222834
        0.1
        0.3
        56.6%
        1.10
        11.2M
        38.3%
        0.40%
        1.4M
        22.5M
        100.0%
        100.0%
        0.0%
        22.5M
        23.8M
        23.8M
        100.0%
        11.5M
        11.2M
        97.9%
        10.6M
        92.3%
        0.6M
        SRX7222834_1
        77.8%
        42.0%
        150bp
        150bp
        10%
        11.5M
        0.7%
        77.8%
        42.0%
        149bp
        150bp
        20%
        11.5M
        SRX7222834_2
        73.9%
        43.0%
        150bp
        150bp
        20%
        11.5M
        2.1%
        74.0%
        43.0%
        147bp
        150bp
        20%
        11.5M
        SRX7222835
        0.0
        2.8
        68.6%
        1.61
        5.5M
        0.0%
        0.48%
        9.9M
        5.5M
        100.0%
        0.0%
        13.7%
        5.5M
        15.5M
        15.5M
        100.0%
        6.1M
        5.5M
        90.7%
        2.5M
        41.2%
        3.0M
        50.1%
        44.0%
        23bp
        23bp
        20%
        7.5M
        1.9%
        48.5%
        44.0%
        24bp
        23bp
        20%
        6.1M
        SRX7222836
        0.1
        0.0
        56.9%
        1.06
        10.5M
        38.5%
        0.24%
        1.4M
        21.0M
        100.0%
        100.0%
        0.0%
        21.0M
        22.4M
        22.4M
        100.0%
        10.6M
        10.5M
        99.2%
        9.9M
        93.7%
        0.6M
        SRX7222836_1
        76.6%
        42.0%
        150bp
        150bp
        10%
        10.6M
        0.6%
        76.6%
        42.0%
        149bp
        150bp
        20%
        10.6M
        SRX7222836_2
        75.7%
        42.0%
        150bp
        150bp
        40%
        10.6M
        0.9%
        75.7%
        42.0%
        149bp
        150bp
        40%
        10.6M
        SRX7222837
        0.1
        0.0
        59.0%
        1.00
        12.3M
        36.3%
        0.23%
        1.6M
        24.5M
        100.0%
        100.0%
        0.0%
        24.5M
        26.1M
        26.1M
        100.0%
        12.5M
        12.3M
        98.5%
        11.5M
        92.5%
        0.8M
        SRX7222837_1
        78.7%
        42.0%
        150bp
        150bp
        10%
        12.5M
        0.6%
        78.7%
        42.0%
        149bp
        150bp
        20%
        12.5M
        SRX7222837_2
        78.2%
        42.0%
        150bp
        150bp
        40%
        12.5M
        0.9%
        78.3%
        42.0%
        149bp
        150bp
        40%
        12.5M
        SRX7222838
        0.1
        0.0
        57.7%
        0.98
        10.3M
        37.8%
        0.24%
        1.2M
        20.7M
        100.0%
        100.0%
        0.0%
        20.7M
        21.9M
        21.9M
        100.0%
        10.5M
        10.3M
        98.3%
        9.8M
        92.8%
        0.6M
        SRX7222838_1
        77.6%
        42.0%
        150bp
        150bp
        10%
        10.5M
        0.6%
        77.6%
        42.0%
        149bp
        150bp
        20%
        10.5M
        SRX7222838_2
        76.6%
        42.0%
        150bp
        150bp
        40%
        10.5M
        0.9%
        76.6%
        42.0%
        149bp
        150bp
        40%
        10.5M
        SRX7222839
        0.1
        0.0
        56.3%
        1.02
        12.0M
        39.5%
        0.24%
        1.3M
        24.0M
        100.0%
        100.0%
        0.0%
        24.0M
        25.3M
        25.3M
        100.0%
        12.1M
        12.0M
        99.2%
        11.4M
        94.4%
        0.6M
        SRX7222839_1
        77.7%
        42.0%
        150bp
        150bp
        10%
        12.1M
        0.6%
        77.7%
        42.0%
        149bp
        150bp
        20%
        12.1M
        SRX7222839_2
        76.5%
        42.0%
        150bp
        150bp
        30%
        12.1M
        0.9%
        76.5%
        42.0%
        149bp
        150bp
        30%
        12.1M
        SRX7222840
        0.0
        2.3
        71.1%
        1.69
        5.6M
        0.0%
        0.42%
        9.9M
        5.6M
        100.0%
        0.0%
        13.2%
        5.6M
        15.6M
        15.6M
        100.0%
        6.0M
        5.6M
        94.2%
        2.5M
        42.5%
        3.1M
        54.3%
        43.0%
        23bp
        23bp
        30%
        7.1M
        1.7%
        54.8%
        43.0%
        24bp
        23bp
        40%
        6.0M
        SRX7222841
        0.0
        2.6
        75.8%
        1.39
        7.1M
        0.0%
        0.42%
        13.1M
        7.1M
        100.0%
        0.0%
        14.7%
        7.1M
        20.3M
        20.3M
        100.0%
        7.6M
        7.1M
        93.8%
        3.1M
        40.7%
        4.0M
        62.3%
        44.0%
        24bp
        24bp
        40%
        8.5M
        1.6%
        64.0%
        44.0%
        24bp
        23bp
        40%
        7.6M
        SRX7222842
        0.0
        3.6
        76.0%
        1.66
        7.4M
        0.0%
        0.42%
        11.9M
        7.4M
        100.0%
        0.0%
        12.2%
        7.4M
        19.3M
        19.3M
        100.0%
        7.9M
        7.4M
        94.6%
        3.0M
        38.0%
        4.4M
        61.6%
        45.0%
        24bp
        24bp
        30%
        8.6M
        1.6%
        63.1%
        45.0%
        24bp
        23bp
        30%
        7.9M
        SRX7222843
        0.0
        1.2
        69.6%
        1.71
        3.6M
        0.0%
        0.45%
        8.3M
        3.6M
        100.0%
        0.0%
        20.3%
        3.6M
        12.0M
        12.0M
        100.0%
        3.9M
        3.6M
        93.0%
        1.7M
        44.0%
        1.9M
        52.9%
        44.0%
        24bp
        24bp
        30%
        4.4M
        1.7%
        53.4%
        44.0%
        24bp
        24bp
        30%
        3.9M
        SRX7222844
        0.0
        1.0
        76.4%
        1.52
        9.4M
        0.0%
        0.39%
        18.9M
        9.4M
        100.0%
        0.0%
        16.4%
        9.4M
        28.3M
        28.3M
        100.0%
        10.0M
        9.4M
        93.9%
        4.6M
        45.6%
        4.9M
        59.3%
        44.0%
        24bp
        24bp
        30%
        11.3M
        1.7%
        59.7%
        44.0%
        25bp
        24bp
        30%
        10.0M
        SRX7222845
        0.0
        1.6
        73.5%
        1.73
        6.7M
        0.0%
        0.46%
        12.7M
        6.7M
        100.0%
        0.0%
        15.8%
        6.7M
        19.5M
        19.5M
        100.0%
        7.3M
        6.7M
        92.7%
        3.1M
        42.5%
        3.7M
        52.4%
        44.0%
        24bp
        24bp
        20%
        8.5M
        1.7%
        52.3%
        45.0%
        25bp
        24bp
        30%
        7.3M
        SRX7222846
        0.1
        6.2
        71.8%
        2.41
        5.0M
        0.0%
        0.99%
        8.5M
        5.0M
        100.0%
        0.0%
        13.4%
        5.0M
        13.6M
        13.6M
        100.0%
        5.7M
        5.0M
        87.7%
        1.9M
        33.5%
        3.1M
        53.5%
        46.0%
        23bp
        23bp
        20%
        5.9M
        2.4%
        55.6%
        46.0%
        23bp
        23bp
        30%
        5.7M
        SRX7734280
        0.1
        0.0
        60.1%
        1.08
        12.4M
        35.3%
        0.30%
        1.6M
        24.8M
        100.0%
        100.0%
        0.0%
        24.8M
        26.4M
        26.4M
        100.0%
        12.6M
        12.4M
        98.4%
        11.7M
        92.5%
        0.7M
        SRX7734280_1
        79.7%
        43.0%
        150bp
        150bp
        20%
        12.6M
        0.8%
        79.7%
        43.0%
        148bp
        150bp
        30%
        12.6M
        SRX7734280_2
        76.0%
        43.0%
        150bp
        150bp
        30%
        12.6M
        1.6%
        76.1%
        43.0%
        147bp
        150bp
        30%
        12.6M
        SRX7734281
        0.1
        0.1
        60.3%
        1.04
        11.7M
        34.0%
        0.35%
        2.4M
        23.5M
        100.0%
        99.9%
        0.0%
        23.5M
        25.8M
        25.8M
        100.0%
        12.0M
        11.7M
        97.9%
        10.9M
        90.5%
        0.9M
        SRX7734281_1
        80.8%
        42.0%
        150bp
        150bp
        20%
        12.1M
        0.7%
        80.8%
        42.0%
        149bp
        150bp
        30%
        12.0M
        SRX7734281_2
        75.7%
        43.0%
        150bp
        150bp
        30%
        12.1M
        3.3%
        76.0%
        43.0%
        146bp
        150bp
        30%
        12.0M
        SRX7734282
        0.1
        0.0
        57.7%
        1.08
        11.7M
        37.4%
        0.36%
        1.5M
        23.4M
        100.0%
        100.0%
        0.0%
        23.4M
        24.9M
        24.9M
        100.0%
        11.9M
        11.7M
        98.0%
        11.0M
        92.5%
        0.7M
        SRX7734282_1
        78.0%
        42.0%
        150bp
        150bp
        20%
        11.9M
        0.8%
        78.0%
        42.0%
        149bp
        150bp
        30%
        11.9M
        SRX7734282_2
        75.9%
        42.0%
        150bp
        150bp
        30%
        11.9M
        1.6%
        75.9%
        42.0%
        148bp
        150bp
        30%
        11.9M
        SRX7734283
        0.1
        0.0
        56.7%
        1.04
        12.5M
        38.9%
        0.29%
        1.5M
        25.0M
        100.0%
        100.0%
        0.0%
        25.0M
        26.4M
        26.4M
        100.0%
        12.6M
        12.5M
        99.1%
        11.8M
        93.7%
        0.7M
        SRX7734283_1
        78.6%
        41.0%
        150bp
        150bp
        30%
        12.6M
        0.6%
        78.6%
        41.0%
        149bp
        150bp
        30%
        12.6M
        SRX7734283_2
        75.7%
        42.0%
        150bp
        150bp
        30%
        12.6M
        1.2%
        75.8%
        42.0%
        148bp
        150bp
        30%
        12.6M
        SRX7734284
        0.1
        0.1
        57.8%
        1.09
        13.4M
        36.6%
        0.39%
        2.2M
        26.8M
        100.0%
        100.0%
        0.0%
        26.8M
        28.9M
        28.9M
        100.0%
        13.6M
        13.4M
        98.8%
        12.4M
        91.4%
        1.0M
        SRX7734284_1
        78.0%
        42.0%
        150bp
        150bp
        20%
        13.6M
        0.8%
        78.0%
        42.0%
        148bp
        150bp
        20%
        13.6M
        SRX7734284_2
        75.2%
        42.0%
        150bp
        150bp
        40%
        13.6M
        2.5%
        75.2%
        42.0%
        146bp
        150bp
        40%
        13.6M
        SRX7734285
        0.1
        0.0
        59.0%
        1.05
        10.6M
        36.9%
        0.29%
        1.1M
        21.1M
        100.0%
        100.0%
        0.0%
        21.1M
        22.2M
        22.2M
        100.0%
        10.8M
        10.6M
        97.6%
        10.1M
        93.1%
        0.5M
        SRX7734285_1
        77.6%
        43.0%
        150bp
        150bp
        20%
        10.9M
        1.2%
        77.6%
        43.0%
        148bp
        150bp
        30%
        10.8M
        SRX7734285_2
        75.2%
        43.0%
        150bp
        150bp
        30%
        10.9M
        2.1%
        75.3%
        43.0%
        147bp
        150bp
        30%
        10.8M
        SRX7734286
        0.1
        0.0
        62.1%
        1.04
        13.2M
        33.7%
        0.44%
        1.6M
        26.3M
        100.0%
        99.9%
        0.0%
        26.3M
        28.0M
        28.0M
        100.0%
        13.4M
        13.2M
        98.5%
        12.4M
        92.8%
        0.8M
        SRX7734286_1
        81.9%
        42.0%
        150bp
        150bp
        30%
        13.4M
        0.7%
        81.9%
        42.0%
        149bp
        150bp
        30%
        13.4M
        SRX7734286_2
        73.6%
        42.0%
        150bp
        150bp
        30%
        13.4M
        2.3%
        73.7%
        42.0%
        147bp
        150bp
        30%
        13.4M
        SRX7734287
        0.0
        0.0
        58.9%
        1.27
        11.2M
        35.8%
        0.30%
        1.7M
        22.4M
        100.0%
        100.0%
        0.1%
        22.4M
        24.1M
        24.1M
        100.0%
        11.3M
        11.2M
        99.0%
        10.4M
        92.2%
        0.8M
        SRX7734287_1
        78.1%
        42.0%
        150bp
        150bp
        20%
        11.3M
        0.6%
        78.2%
        42.0%
        149bp
        150bp
        30%
        11.3M
        SRX7734287_2
        72.6%
        42.0%
        150bp
        150bp
        30%
        11.3M
        1.1%
        72.6%
        42.0%
        148bp
        150bp
        30%
        11.3M
        SRX7734288
        0.1
        0.0
        58.1%
        1.02
        12.4M
        37.0%
        0.33%
        1.8M
        24.9M
        100.0%
        99.9%
        0.0%
        24.9M
        26.7M
        26.7M
        100.0%
        12.8M
        12.5M
        96.9%
        11.6M
        90.2%
        0.9M
        SRX7734288_1
        77.5%
        42.0%
        150bp
        150bp
        10%
        12.9M
        0.7%
        77.5%
        42.0%
        149bp
        150bp
        20%
        12.8M
        SRX7734288_2
        73.7%
        42.0%
        150bp
        150bp
        30%
        12.9M
        3.1%
        73.9%
        42.0%
        146bp
        150bp
        30%
        12.8M
        SRX7734289
        0.1
        0.0
        57.3%
        1.09
        13.7M
        37.6%
        0.35%
        2.1M
        27.4M
        100.0%
        99.9%
        0.0%
        27.4M
        29.6M
        29.6M
        100.0%
        14.1M
        13.7M
        97.3%
        12.8M
        90.4%
        1.0M
        SRX7734289_1
        78.2%
        42.0%
        150bp
        150bp
        20%
        14.2M
        0.6%
        78.2%
        42.0%
        149bp
        150bp
        30%
        14.1M
        SRX7734289_2
        72.6%
        43.0%
        150bp
        150bp
        30%
        14.2M
        3.1%
        72.8%
        43.0%
        146bp
        150bp
        30%
        14.1M
        SRX7734290
        0.1
        0.0
        53.2%
        1.10
        12.6M
        42.7%
        0.33%
        1.1M
        25.2M
        100.0%
        100.0%
        0.0%
        25.2M
        26.3M
        26.3M
        100.0%
        12.8M
        12.6M
        98.7%
        12.1M
        94.9%
        0.5M
        SRX7734290_1
        76.0%
        41.0%
        150bp
        150bp
        30%
        12.8M
        0.7%
        76.0%
        41.0%
        149bp
        150bp
        30%
        12.8M
        SRX7734290_2
        72.0%
        42.0%
        150bp
        150bp
        30%
        12.8M
        1.3%
        72.1%
        42.0%
        148bp
        150bp
        30%
        12.8M
        SRX7734291
        0.1
        0.0
        58.1%
        1.02
        12.9M
        36.8%
        0.37%
        1.9M
        25.9M
        100.0%
        100.0%
        0.0%
        25.9M
        27.8M
        27.8M
        100.0%
        13.2M
        13.0M
        98.2%
        12.1M
        91.8%
        0.8M
        SRX7734291_1
        78.6%
        42.0%
        150bp
        150bp
        20%
        13.2M
        0.8%
        78.6%
        43.0%
        148bp
        150bp
        30%
        13.2M
        SRX7734291_2
        76.4%
        43.0%
        150bp
        150bp
        30%
        13.2M
        1.7%
        76.5%
        43.0%
        147bp
        150bp
        30%
        13.2M

        Sample status checks

        Reports on sample strandedness status, and any failures in trimming or mapping.

        Strandedness Checks

        Showing 0/72 rows and 7/7 columns.
        SampleStatusStrand inference methodProvided strandednessInferred strandednessSense (%)Antisense (%)Unstranded (%)
        SRX7222823
        fail
        RSeQC
        auto
        undetermined
        57.0
        39.5
        3.5
        SRX7222823
        fail
        Salmon
        auto
        forward
        92.4
        7.6
        0.0
        SRX7222824
        fail
        RSeQC
        auto
        undetermined
        54.4
        41.6
        3.9
        SRX7222824
        fail
        Salmon
        auto
        forward
        95.9
        4.1
        0.0
        SRX7222825
        fail
        RSeQC
        auto
        undetermined
        56.6
        39.6
        3.8
        SRX7222825
        fail
        Salmon
        auto
        forward
        86.3
        13.7
        0.0
        SRX7222826
        fail
        RSeQC
        auto
        undetermined
        66.0
        30.1
        3.9
        SRX7222826
        fail
        Salmon
        auto
        forward
        93.8
        6.2
        0.0
        SRX7222827
        fail
        RSeQC
        auto
        undetermined
        57.1
        38.9
        3.9
        SRX7222827
        fail
        Salmon
        auto
        forward
        93.1
        6.9
        0.0
        SRX7222828
        fail
        RSeQC
        auto
        undetermined
        58.5
        37.7
        3.8
        SRX7222828
        fail
        Salmon
        auto
        forward
        82.8
        17.2
        0.0
        SRX7222829
        fail
        RSeQC
        auto
        undetermined
        66.8
        29.3
        3.9
        SRX7222829
        fail
        Salmon
        auto
        forward
        94.8
        5.2
        0.0
        SRX7222830
        fail
        RSeQC
        auto
        undetermined
        56.4
        39.7
        3.8
        SRX7222830
        fail
        Salmon
        auto
        forward
        89.8
        10.2
        0.0
        SRX7222831
        fail
        RSeQC
        auto
        undetermined
        63.8
        32.6
        3.6
        SRX7222831
        fail
        Salmon
        auto
        forward
        89.7
        10.3
        0.0
        SRX7222832
        fail
        RSeQC
        auto
        undetermined
        63.0
        34.0
        3.1
        SRX7222832
        fail
        Salmon
        auto
        forward
        88.5
        11.5
        0.0
        SRX7222833
        pass
        RSeQC
        auto
        reverse
        0.8
        96.4
        2.8
        SRX7222833
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7222834
        pass
        RSeQC
        auto
        reverse
        0.6
        96.7
        2.7
        SRX7222834
        pass
        Salmon
        auto
        reverse
        0.6
        99.4
        0.0
        SRX7222835
        fail
        RSeQC
        auto
        undetermined
        58.3
        37.9
        3.7
        SRX7222835
        fail
        Salmon
        auto
        forward
        97.9
        2.1
        0.0
        SRX7222836
        pass
        RSeQC
        auto
        reverse
        0.6
        96.7
        2.7
        SRX7222836
        pass
        Salmon
        auto
        reverse
        0.4
        99.6
        0.0
        SRX7222837
        pass
        RSeQC
        auto
        reverse
        0.7
        97.0
        2.3
        SRX7222837
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7222838
        pass
        RSeQC
        auto
        reverse
        0.8
        96.9
        2.3
        SRX7222838
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7222839
        pass
        RSeQC
        auto
        reverse
        0.6
        96.8
        2.6
        SRX7222839
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7222840
        fail
        RSeQC
        auto
        undetermined
        59.9
        36.4
        3.7
        SRX7222840
        fail
        Salmon
        auto
        forward
        83.1
        16.9
        0.0
        SRX7222841
        fail
        RSeQC
        auto
        undetermined
        60.7
        35.5
        3.8
        SRX7222841
        fail
        Salmon
        auto
        forward
        86.4
        13.6
        0.0
        SRX7222842
        fail
        RSeQC
        auto
        undetermined
        64.1
        32.0
        3.9
        SRX7222842
        fail
        Salmon
        auto
        forward
        86.1
        13.9
        0.0
        SRX7222843
        fail
        RSeQC
        auto
        undetermined
        57.3
        39.3
        3.4
        SRX7222843
        fail
        Salmon
        auto
        forward
        95.9
        4.1
        0.0
        SRX7222844
        fail
        RSeQC
        auto
        undetermined
        57.0
        38.7
        4.3
        SRX7222844
        fail
        Salmon
        auto
        forward
        94.9
        5.1
        0.0
        SRX7222845
        fail
        RSeQC
        auto
        undetermined
        58.5
        37.6
        4.0
        SRX7222845
        fail
        Salmon
        auto
        forward
        91.0
        9.0
        0.0
        SRX7222846
        fail
        RSeQC
        auto
        undetermined
        56.8
        39.6
        3.6
        SRX7222846
        fail
        Salmon
        auto
        forward
        95.4
        4.6
        0.0
        SRX7734280
        pass
        RSeQC
        auto
        reverse
        0.8
        96.3
        2.9
        SRX7734280
        pass
        Salmon
        auto
        reverse
        0.6
        99.4
        0.0
        SRX7734281
        pass
        RSeQC
        auto
        reverse
        0.6
        96.6
        2.8
        SRX7734281
        pass
        Salmon
        auto
        reverse
        0.7
        99.3
        0.0
        SRX7734282
        pass
        RSeQC
        auto
        reverse
        1.9
        95.2
        2.8
        SRX7734282
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7734283
        pass
        RSeQC
        auto
        reverse
        0.5
        96.3
        3.1
        SRX7734283
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7734284
        pass
        RSeQC
        auto
        reverse
        2.5
        94.3
        3.2
        SRX7734284
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7734285
        pass
        RSeQC
        auto
        reverse
        1.3
        95.9
        2.8
        SRX7734285
        pass
        Salmon
        auto
        reverse
        0.6
        99.4
        0.0
        SRX7734286
        pass
        RSeQC
        auto
        reverse
        0.8
        96.2
        3.0
        SRX7734286
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7734287
        pass
        RSeQC
        auto
        reverse
        3.3
        93.4
        3.3
        SRX7734287
        pass
        Salmon
        auto
        reverse
        0.4
        99.6
        0.0
        SRX7734288
        pass
        RSeQC
        auto
        reverse
        0.6
        96.1
        3.3
        SRX7734288
        pass
        Salmon
        auto
        reverse
        0.6
        99.4
        0.0
        SRX7734289
        pass
        RSeQC
        auto
        reverse
        0.4
        95.9
        3.7
        SRX7734289
        pass
        Salmon
        auto
        reverse
        0.6
        99.4
        0.0
        SRX7734290
        pass
        RSeQC
        auto
        reverse
        1.0
        95.6
        3.4
        SRX7734290
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0
        SRX7734291
        pass
        RSeQC
        auto
        reverse
        1.7
        95.2
        3.1
        SRX7734291
        pass
        Salmon
        auto
        reverse
        0.5
        99.5
        0.0

        FastQC (raw)

        This section of the report shows FastQC results before adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        CTCGTTTTTTACTAAACTAGATCTAGACTAACACTAACGAATTATCCATT
        18
        795523
        0.1369%
        CTCAACAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTCATGCA
        18
        701366
        0.1207%
        ATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAATAATAT
        18
        1050019
        0.1807%
        AGCAGCTACAATGTTGTAAGTTTCTTCTTCTTGCCCGAATCTGTAACCTT
        18
        619313
        0.1066%
        GGAGCCTCAACAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTC
        18
        487953
        0.0840%
        GTGAGCATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAA
        18
        954788
        0.1643%
        CGCCGAATACACCAGCTACACCTAACATGTGAAATGGGTGCATAAGAATG
        18
        538097
        0.0926%
        CGGCCAAGCCGCTAAGAAGAAATGTAAAGAACGAGAATTGTTGAAACTAG
        18
        360455
        0.0620%
        GCATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAATAAT
        18
        609345
        0.1049%
        GAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACCAAGGATTT
        18
        2069789
        0.3562%
        CAATTATCTACTTAGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAA
        18
        2316915
        0.3987%
        AGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACCAAGGATTTT
        18
        739318
        0.1272%
        AGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACCAAGGATT
        18
        947004
        0.1630%
        CAACATTCTTATGCACCCATTTCACATGTTAGGTGTAGCTGGTGTATTCG
        18
        561416
        0.0966%
        GTTTTTCTGATGGTATGCCTCTAGGAATCTCTGGTACTTTCAACTTTATG
        18
        705925
        0.1215%
        GAAACTTACAACATTGTAGCTGCTCACGGTTATTTTGGCCGATTGATTTT
        18
        615438
        0.1059%
        GGGAACTTAGTTTCCGTCTGGGTATGCGTCCTTGGATTGCTGTTGCATAT
        18
        346421
        0.0596%
        CTCGTTCTTTACATTTCTTCTTAGCGGCTTGGCCGGTAGTAGGTATTTGG
        18
        575986
        0.0991%
        CAAATATCATGGTCTAATAAAGAATAATTCTGATTAGTTGATAATTTTGT
        18
        430190
        0.0740%
        TCTACTTAGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACC
        18
        510051
        0.0878%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Cutadapt

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        FastQC (trimmed)

        This section of the report shows FastQC results after adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GTGAGCATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAA
        18
        953241
        0.1682%
        CTCGTTTTTTACTAAACTAGATCTAGACTAACACTAACGAATTATCCATT
        18
        794414
        0.1402%
        ATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAATAATAT
        18
        1048238
        0.1849%
        AGCAGCTACAATGTTGTAAGTTTCTTCTTCTTGCCCGAATCTGTAACCTT
        18
        618355
        0.1091%
        GCATTACGTTCATGCATAACTTCCATACCAAGGTTAGCACGGTTAATAAT
        18
        608194
        0.1073%
        CTCAACAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTCATGCA
        18
        700042
        0.1235%
        CGCCGAATACACCAGCTACACCTAACATGTGAAATGGGTGCATAAGAATG
        18
        537020
        0.0947%
        GGAGCCTCAACAGCAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTC
        18
        486932
        0.0859%
        CGGCCAAGCCGCTAAGAAGAAATGTAAAGAACGAGAATTGTTGAAACTAG
        18
        359736
        0.0635%
        TTTGGATTGAAGGGAGCTCT
        18
        1511545
        0.2667%
        TTCATGGACGTTGATAAGATCTTTC
        18
        1279394
        0.2257%
        AGTTACTAATTCATGATCTGGC
        18
        1536112
        0.2710%
        CAATTATCTACTTAGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAA
        18
        2316868
        0.4088%
        GAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACCAAGGATTT
        18
        2069688
        0.3652%
        AGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACCAAGGATT
        18
        946960
        0.1671%
        CTCGTTCTTTACATTTCTTCTTAGCGGCTTGGCCGGTAGTAGGTATTTGG
        18
        575960
        0.1016%
        GTTTTTCTGATGGTATGCCTCTAGGAATCTCTGGTACTTTCAACTTTATG
        18
        705812
        0.1245%
        GAAACTTACAACATTGTAGCTGCTCACGGTTATTTTGGCCGATTGATTTT
        18
        615394
        0.1086%
        CAACATTCTTATGCACCCATTTCACATGTTAGGTGTAGCTGGTGTATTCG
        18
        561397
        0.0991%
        TCTACTTAGAGAATTTGTGCGCTTGGGAGTCCCTGATTATTAAATAAACC
        18
        510038
        0.0900%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        DupRadar

        DupRadar provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.URL: bioconductor.org/packages/release/bioc/html/dupRadar.html

        Created with MultiQC

        Picard

        Tools for manipulating high-throughput sequencing data.URL: http://broadinstitute.github.io/picard

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        Created with MultiQC

        QualiMap

        Quality control of alignment data and its derivatives like feature counts.URL: http://qualimap.bioinfo.cipf.esDOI: 10.1093/bioinformatics/btv566; 10.1093/bioinformatics/bts503

        Genomic origin of reads

        Classification of mapped reads as originating in exonic, intronic or intergenic regions. These can be displayed as either the number or percentage of mapped reads.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. This allows mapped reads to be grouped by whether they originate in an exonic region (for QualiMap, this may include 5′ and 3′ UTR regions as well as protein-coding exons), an intron, or an intergenic region (see the Qualimap 2 documentation).

        The inferred genomic origins of RNA-seq reads are presented here as a bar graph showing either the number or percentage of mapped reads in each read dataset that have been assigned to each type of genomic region. This graph can be used to assess the proportion of useful reads in an RNA-seq experiment. That proportion can be reduced by the presence of intron sequences, especially if depletion of ribosomal RNA was used during sample preparation (Sims et al. 2014). It can also be reduced by off-target transcripts, which are detected in greater numbers at the sequencing depths needed to detect poorly-expressed transcripts (Tarazona et al. 2011).

        Created with MultiQC

        Gene Coverage Profile

        Mean distribution of coverage depth across the length of all mapped transcripts.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. QualiMap uses this information to calculate the depth of coverage along the length of each annotated transcript. For a set of reads mapped to a transcript, the depth of coverage at a given base position is the number of high-quality reads that map to the transcript at that position (Sims et al. 2014).

        QualiMap calculates coverage depth at every base position of each annotated transcript. To enable meaningful comparison between transcripts, base positions are rescaled to relative positions expressed as percentage distance along each transcript (0%, 1%, …, 99%). For the set of transcripts with at least one mapped read, QualiMap plots the cumulative mapped-read depth (y-axis) at each relative transcript position (x-axis). This plot shows the gene coverage profile across all mapped transcripts for each read dataset. It provides a visual way to assess positional biases, such as an accumulation of mapped reads at the 3′ end of transcripts, which may indicate poor RNA quality in the original sample (Conesa et al. 2016).

        The Normalised plot is calculated by MultiQC to enable comparison of samples with varying sequencing depth. The cumulative mapped-read depth at each position across the averaged transcript position are divided by the total for that sample across the entire averaged transcript.

        Created with MultiQC

        RSeQC

        Evaluates high throughput RNA-seq data.URL: http://rseqc.sourceforge.netDOI: 10.1093/bioinformatics/bts356

        Read Distribution

        Read Distribution calculates how mapped reads are distributed over genome features.

        Created with MultiQC

        Inner Distance

        Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

        Created with MultiQC

        Read Duplication

        read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

        Created with MultiQC

        Junction Annotation

        Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

        Created with MultiQC

        Junction Saturation

        Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

        Click a line to see the data side by side (as in the original RSeQC plot).

        Created with MultiQC

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Created with MultiQC

        Bam Stat

        All numbers reported in millions.

        Created with MultiQC

        Samtools

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Percent mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

        Created with MultiQC

        Alignment stats

        This module parses the output from samtools stats. All numbers in millions.

        Created with MultiQC

        Flagstat

        This module parses the output from samtools flagstat

        Created with MultiQC

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Created with MultiQC

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 0/36 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        SRX7222823
        4.4M
        4.1M
        94.1%
        1.7M
        39.9%
        2.4M
        22.0bp
        22.3bp
        0.1M
        0.0M
        0.1M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222824
        7.2M
        6.5M
        91.1%
        2.8M
        38.4%
        3.8M
        21.0bp
        21.3bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222825
        9.5M
        8.6M
        90.8%
        3.1M
        32.3%
        5.5M
        21.0bp
        21.2bp
        0.3M
        0.1M
        0.3M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222826
        7.2M
        6.6M
        91.0%
        2.3M
        32.4%
        4.2M
        24.0bp
        23.4bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222827
        9.0M
        7.9M
        88.2%
        3.3M
        37.4%
        4.6M
        24.0bp
        23.1bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222828
        7.8M
        6.9M
        88.7%
        2.6M
        33.5%
        4.3M
        22.0bp
        21.8bp
        0.3M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222829
        7.3M
        6.6M
        90.2%
        2.4M
        33.3%
        4.2M
        25.0bp
        23.6bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222830
        8.0M
        7.3M
        90.8%
        3.1M
        38.0%
        4.3M
        22.0bp
        21.8bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222831
        10.1M
        8.7M
        85.4%
        3.1M
        30.5%
        5.6M
        23.0bp
        22.5bp
        0.3M
        0.2M
        0.3M
        0.0M
        0.0M
        0.0M
        1.0%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222832
        2.4M
        2.0M
        84.3%
        0.7M
        29.8%
        1.3M
        24.0bp
        22.8bp
        0.1M
        0.0M
        0.1M
        0.0M
        0.0M
        0.0M
        1.0%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222833
        11.4M
        11.3M
        99.4%
        10.8M
        94.7%
        0.5M
        297.0bp
        297.4bp
        4.1M
        4.1M
        4.0M
        0.0M
        0.1M
        0.0M
        0.2%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7222834
        11.5M
        11.2M
        97.9%
        10.6M
        92.3%
        0.6M
        296.0bp
        294.6bp
        4.0M
        4.0M
        3.9M
        0.1M
        0.0M
        0.0M
        0.4%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7222835
        6.1M
        5.5M
        90.7%
        2.5M
        41.2%
        3.0M
        24.0bp
        22.7bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        1.3bp
        0.0%
        1.1bp
        SRX7222836
        10.6M
        10.5M
        99.2%
        9.9M
        93.7%
        0.6M
        297.0bp
        297.4bp
        3.7M
        3.7M
        3.6M
        0.0M
        0.0M
        0.0M
        0.2%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7222837
        12.5M
        12.3M
        98.5%
        11.5M
        92.5%
        0.8M
        297.0bp
        297.3bp
        3.8M
        3.8M
        3.7M
        0.0M
        0.1M
        0.0M
        0.2%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7222838
        10.5M
        10.3M
        98.3%
        9.8M
        92.8%
        0.6M
        297.0bp
        297.4bp
        3.4M
        3.4M
        3.2M
        0.1M
        0.0M
        0.0M
        0.2%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7222839
        12.1M
        12.0M
        99.2%
        11.4M
        94.4%
        0.6M
        297.0bp
        297.3bp
        4.3M
        4.3M
        4.2M
        0.0M
        0.1M
        0.0M
        0.2%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7222840
        6.0M
        5.6M
        94.2%
        2.5M
        42.5%
        3.1M
        23.0bp
        22.9bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.1bp
        0.0%
        1.1bp
        SRX7222841
        7.6M
        7.1M
        93.8%
        3.1M
        40.7%
        4.0M
        23.0bp
        23.0bp
        0.1M
        0.0M
        0.1M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222842
        7.9M
        7.4M
        94.6%
        3.0M
        38.0%
        4.4M
        23.0bp
        22.9bp
        0.1M
        0.0M
        0.1M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222843
        3.9M
        3.6M
        93.0%
        1.7M
        44.0%
        1.9M
        24.0bp
        23.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222844
        10.0M
        9.4M
        93.9%
        4.6M
        45.6%
        4.9M
        24.0bp
        23.7bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7222845
        7.3M
        6.7M
        92.7%
        3.1M
        42.5%
        3.7M
        24.0bp
        23.2bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        1.1bp
        0.0%
        1.0bp
        SRX7222846
        5.7M
        5.0M
        87.7%
        1.9M
        33.5%
        3.1M
        22.0bp
        21.9bp
        0.2M
        0.1M
        0.2M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        1.2bp
        0.0%
        1.0bp
        SRX7734280
        12.6M
        12.4M
        98.4%
        11.7M
        92.5%
        0.7M
        296.0bp
        295.8bp
        4.7M
        4.7M
        4.6M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734281
        12.0M
        11.7M
        97.9%
        10.9M
        90.5%
        0.9M
        294.0bp
        293.6bp
        4.4M
        4.4M
        4.3M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734282
        11.9M
        11.7M
        98.0%
        11.0M
        92.5%
        0.7M
        296.0bp
        295.9bp
        4.2M
        4.2M
        4.1M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734283
        12.6M
        12.5M
        99.1%
        11.8M
        93.7%
        0.7M
        297.0bp
        296.8bp
        4.6M
        4.6M
        4.5M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7734284
        13.6M
        13.4M
        98.8%
        12.4M
        91.4%
        1.0M
        295.0bp
        294.3bp
        4.7M
        4.7M
        4.6M
        0.0M
        0.1M
        0.0M
        0.4%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734285
        10.8M
        10.6M
        97.6%
        10.1M
        93.1%
        0.5M
        295.0bp
        294.7bp
        3.6M
        3.6M
        3.5M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734286
        13.4M
        13.2M
        98.5%
        12.4M
        92.8%
        0.8M
        295.0bp
        294.7bp
        4.7M
        4.7M
        4.6M
        0.0M
        0.1M
        0.0M
        0.4%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734287
        11.3M
        11.2M
        99.0%
        10.4M
        92.2%
        0.8M
        297.0bp
        296.9bp
        3.8M
        3.8M
        3.6M
        0.2M
        0.1M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp
        SRX7734288
        12.8M
        12.5M
        96.9%
        11.6M
        90.2%
        0.9M
        295.0bp
        293.9bp
        5.0M
        5.0M
        4.8M
        0.1M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7734289
        14.1M
        13.7M
        97.3%
        12.8M
        90.4%
        1.0M
        294.0bp
        293.7bp
        6.1M
        6.1M
        6.0M
        0.1M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7734290
        12.8M
        12.6M
        98.7%
        12.1M
        94.9%
        0.5M
        297.0bp
        296.4bp
        5.2M
        5.2M
        5.0M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.3bp
        SRX7734291
        13.2M
        13.0M
        98.2%
        12.1M
        91.8%
        0.8M
        296.0bp
        295.7bp
        4.6M
        4.6M
        4.5M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        1.4bp
        0.0%
        1.2bp

        Alignment Scores

        Created with MultiQC

        Sample relationships

        Plots interrogating sample relationships, based on final count matrices.

        STAR_SALMON DESeq2 sample similarity

        Created with MultiQC

        STAR_SALMON DESeq2 PCA plot

        Created with MultiQC

        Biotype Counts

        Biotype Counts shows reads overlapping genomic features of different biotypes, counted by featureCounts.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BEDTOOLS_GENOMECOV_FWbedtools2.31.1
        CUSTOM_GETCHROMSIZESgetchromsizes1.21
        CUSTOM_TX2GENEpython3.10.4
        DESEQ2_QC_STAR_SALMONbioconductor-deseq21.28.0
        r-base4.0.3
        DupRadarbioconductor-dupradar1.32.0
        FASTQCfastqc0.12.1
        FQ_LINTfq0.12.0 (2024-07-08)
        FQ_SUBSAMPLEfq0.12.0 (2024-07-08)
        GTF2BEDperl5.26.2
        GTF_FILTERpython3.9.5
        GUNZIP_FASTAgunzip1.1
        GUNZIP_GTFgunzip1.1
        MAKE_TRANSCRIPTS_FASTArsem1.3.1
        star2.7.10a
        MULTIQC_CUSTOM_BIOTYPEpython3.9.5
        PICARD_MARKDUPLICATESpicard3.1.1
        QUALIMAP_RNASEQqualimap2.3
        RSEQC_BAMSTATrseqc5.0.2
        RSEQC_INFEREXPERIMENTrseqc5.0.2
        RSEQC_INNERDISTANCErseqc5.0.2
        RSEQC_JUNCTIONANNOTATIONrseqc5.0.2
        RSEQC_JUNCTIONSATURATIONrseqc5.0.2
        RSEQC_READDISTRIBUTIONrseqc5.0.2
        RSEQC_READDUPLICATIONrseqc5.0.2
        SALMON_INDEXsalmon1.10.3
        SALMON_QUANTsalmon1.10.3
        SAMTOOLS_FLAGSTATsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        SE_GENEbioconductor-summarizedexperiment1.32.0
        STAR_ALIGNgawk5.1.0
        samtools1.21
        star2.7.11b
        STAR_GENOMEGENERATEgawk5.1.0
        samtools1.21
        star2.7.11b
        STRINGTIE_STRINGTIEstringtie2.2.3
        SUBREAD_FEATURECOUNTSsubread2.0.6
        TRIMGALOREcutadapt4.9
        trimgalore0.6.10
        TXIMETA_TXIMPORTbioconductor-tximeta1.20.1
        UCSC_BEDCLIPucsc377
        UCSC_BEDGRAPHTOBIGWIGucsc469
        WorkflowNextflow24.10.1
        nf-core/rnaseqv3.18.0-gb96a753

        nf-core/rnaseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnaseq

        Methods

        Data was processed using nf-core/rnaseq v3.18.0 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.1 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/rnaseq --input samplesheet_rnaseq.csv --fasta /work/zarski/for_hiwi/arabid_genome/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz --gtf /work/zarski/for_hiwi/arabid_genome/Arabidopsis_thaliana.TAIR10.60.gtf.gz -profile singularity --outdir /work/zarski/arabid_tiwari

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/rnaseq Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/rnaseq

        Input/output options

        input
        samplesheet_rnaseq.csv
        outdir
        /work/zarski/arabid_tiwari

        Reference genome options

        fasta
        /work/zarski/for_hiwi/arabid_genome/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
        gtf
        /work/zarski/for_hiwi/arabid_genome/Arabidopsis_thaliana.TAIR10.60.gtf.gz

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        singularity
        launchDir
        /gpfs1/work/zarski/arabid_tiwari/skripts
        profile
        singularity
        projectDir
        /home/zarski/.nextflow/assets/nf-core/rnaseq
        revision
        master
        runName
        desperate_brown
        userName
        zarski
        workDir
        /gpfs1/work/zarski/arabid_tiwari/skripts/work